jigcell.compare.data
Class PackedTreeDataElement2

java.lang.Object
  javax.swing.TransferHandler
      jigcell.compare.impl.Transferer
          jigcell.compare.data.DataElement
              jigcell.compare.data.EditableDataElement
                  jigcell.compare.data.TreeDataElement
                      jigcell.compare.data.PackedTreeDataElement
                          jigcell.compare.data.PackedTreeDataElement2

All Implemented Interfaces:

java.awt.datatransfer.Transferable, java.io.Serializable, IDataElement, IEditableDataElement

public class PackedTreeDataElement2
extends PackedTreeDataElement

An implementation of EditableDataElement that uses an AVL tree to store values. The tree keys are primitives. Each key can hold a pack of values so this structure uses less memory than SparseTreeDataElement2 for dense collections. The size of the pack is adjustable. This structure becomes faster and smaller than PackedTreeDataElement around 25 times the pack size entries. PackedTreeDataElement2 does not protect against concurrent edits. The maximum number of values this element can contain is approximately 2^40, but is likely to fail before then.

This code is licensed under the DARPA BioCOMP Open Source License. See LICENSE for more details.

Author:

Nicholas Allen

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class jigcell.compare.data.EditableDataElement

EditableDataElement.EditableDataElementDelegate

Nested classes/interfaces inherited from interface jigcell.compare.IDataElement

IDataElement.Type

Field Summary

private it.unimi.dsi.fastutil.longs.ModifiedLong2ObjectAVLTreeMap

values Element values

Fields inherited from class jigcell.compare.data.PackedTreeDataElement

MESSAGE_CHUNKSIZEERROR, MESSAGE_LASTERROR, size, SIZE_DEFAULTPACK

Fields inherited from class jigcell.compare.data.TreeDataElement

length

Fields inherited from class jigcell.compare.data.EditableDataElement

DOUBLE_NaN, DOUBLE_NINFINITY, DOUBLE_PINFINITY, MESSAGE_PARSEBLOCKERROR, MESSAGE_PARSEERROR, MESSAGE_PARSEEXTRAERROR, MESSAGE_PARSELITERALERROR, PATTERN_FP, prototypeChild, TOKEN_ALL, TOKEN_BLOCKELEMENT, TOKEN_BLOCKEND, TOKEN_BLOCKSTART, TOKEN_LITERAL

Fields inherited from class jigcell.compare.data.DataElement

lockCount, LONGPOOL, PATTERN_FALSE, PATTERN_NAN, PATTERN_NINFINITY, PATTERN_NINFINITY2, PATTERN_NULL, PATTERN_PINFINITY, PATTERN_PINFINITY2, PATTERN_TRUE, PATTERN_VOID, SIZE_LONGPOOL

Fields inherited from class jigcell.compare.impl.Transferer

CSV_FOOTER, CSV_LINEPOSTPEND, CSV_LINEPREPEND, CSV_LINESEPARATOR, HTML_FOOTER, HTML_HEADPOSTPEND, HTML_HEADPREPEND, HTML_HEADSEPARATOR, HTML_LINEPOSTPEND, HTML_LINEPREPEND, HTML_LINESEPARATOR

Fields inherited from class javax.swing.TransferHandler

COPY, COPY_OR_MOVE, MOVE, NONE

Constructor Summary

PackedTreeDataElement2()
Creates a new data element backed by a tree with packed storage.

PackedTreeDataElement2(int size)
Creates a new data element with packed storage.

Method Summary

protected EditableDataElement	constructNew() Constructs a new element of the same type as this element.
static IEditableDataElement	createElement(java.io.Reader reader) Generates a PackedTreeDataElement2 from streaming input.
static IEditableDataElement	createElementSafe(java.io.Reader reader) Generates a PackedTreeDataElement2 from streaming input.
protected java.lang.Object	getDirect(long pos) Gets the value at a position. Boolean values are represented by Boolean. Empty values are represented by null. Integral values are represented by Integer. Literal values are represented by String. Multiple values are represented by DataElement. Real values are represented by Double. The position of the object may be anything.
protected long	lastValue() Finds the last defined value.
protected void	putDirect(long pos, java.lang.Object value) Sets the value at a position. Boolean values are represented by Boolean. Empty values are represented by null. Integral values are represented by Integer. Literal values are represented by String. Multiple values are represented by DataElement. Real values are represented by Double. The position of the object may be anything.
protected void	removeDirect(long pos) Removes the value at a position. The position of the object may be anything.

Methods inherited from class jigcell.compare.data.TreeDataElement

clear, getLength, getValues, isAvailable, memoryLock, memoryUnlock, setLengthDirect, setValue, setValues, unsetValue

Methods inherited from class jigcell.compare.data.EditableDataElement

copyValue, createElement, createElement, createElement, createElementSafe, createElementSafe, createScalarElement, createScalarElement, createScalarElement, createScalarElement, forceSlice, forceSlice, forceSlice, forceSlice, getBooleanValue, getChecked, getIntegralValue, getListValue, getLiteralValue, getPrototypeChild, getRealValue, getType, getType, makeList, moveValue, putChecked, setPrototypeChild, setValue, setValue, setValue, setValue, setValue, setValue, setValue, setValue, setValue, setValueInterpreted, setValueInterpreted, swapValues

Methods inherited from class jigcell.compare.data.DataElement

forceBooleanValue, forceBooleanValue, forceIntegralValue, forceIntegralValue, forceListValue, forceLiteralValue, forceLiteralValue, forceRealValue, forceRealValue, forceSlice, getBooleanValue, getIntegralValue, getLiteralValue, getLongObject, getRealValue, getSlice, getSlice, getSlice, getSlice, getSlice, getTransferData, isScalar, isSpecialNonNumeric, toString, toString, toString, toString, toString, toString, toString, toString, toString, toString, toString, toString, toString, toString, toString, toString

Methods inherited from class jigcell.compare.impl.Transferer

addExtension, addFlavor, createCSVTable, createFormattedTable, createHTMLTable, getExceptionRecorder, getExpectedClasses, getExpectedClasses, getExpectedClasses, getFlavors, getFlavors, getPreferredExtensions, getPreferredExtensions, getTransferClass, getTransferDataFlavors, getTransferFlavor, isDataFlavorSupported, transfer

Methods inherited from class javax.swing.TransferHandler

canImport, createTransferable, exportAsDrag, exportDone, exportToClipboard, getCopyAction, getCutAction, getPasteAction, getSourceActions, getVisualRepresentation, importData

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface jigcell.compare.IDataElement

forceBooleanValue, forceBooleanValue, forceIntegralValue, forceIntegralValue, forceListValue, forceLiteralValue, forceLiteralValue, forceRealValue, forceRealValue, forceSlice, getBooleanValue, getIntegralValue, getLiteralValue, getRealValue, getSlice, getSlice, getSlice, getSlice, getSlice, isScalar, toString, toString, toString, toString, toString, toString, toString

Methods inherited from interface java.awt.datatransfer.Transferable

getTransferData, getTransferDataFlavors, isDataFlavorSupported

Field Detail

values

private it.unimi.dsi.fastutil.longs.ModifiedLong2ObjectAVLTreeMap values

Element values

Constructor Detail

PackedTreeDataElement2

public PackedTreeDataElement2()

Creates a new data element backed by a tree with packed storage.

PackedTreeDataElement2

public PackedTreeDataElement2(int size)

Creates a new data element with packed storage.

Parameters:

size - Pack size

Method Detail

createElement

public static IEditableDataElement createElement(java.io.Reader reader)

Generates a PackedTreeDataElement2 from streaming input.

Parameters:

reader - Reader

createElementSafe

public static IEditableDataElement createElementSafe(java.io.Reader reader)

Generates a PackedTreeDataElement2 from streaming input. If an element cannot be created, an empty element in returned.

Parameters:

reader - Reader

constructNew

protected EditableDataElement constructNew()

Constructs a new element of the same type as this element.

Overrides:

constructNew in class PackedTreeDataElement

getDirect

protected java.lang.Object getDirect(long pos)

Gets the value at a position. Boolean values are represented by Boolean. Empty values are represented by null. Integral values are represented by Integer. Literal values are represented by String. Multiple values are represented by DataElement. Real values are represented by Double. The position of the object may be anything.

Overrides:

getDirect in class PackedTreeDataElement

Parameters:

pos - Position

lastValue

protected long lastValue()

Finds the last defined value.

Overrides:

lastValue in class PackedTreeDataElement

putDirect

protected void putDirect(long pos,
                         java.lang.Object value)

Sets the value at a position. Boolean values are represented by Boolean. Empty values are represented by null. Integral values are represented by Integer. Literal values are represented by String. Multiple values are represented by DataElement. Real values are represented by Double. The position of the object may be anything.

Overrides:

putDirect in class PackedTreeDataElement

Parameters:

pos - Position

value - Value

removeDirect

protected void removeDirect(long pos)

Removes the value at a position. The position of the object may be anything.

Overrides:

removeDirect in class PackedTreeDataElement

Parameters:

pos - Position